The problem is due to a temporary station that was built for the Port Authority Trans Hudson subway. That station can’t be dismantled to make way for underground freight areas until crews finish the permanent station.

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“Several years there was a design miss,” said Patrick Foye, executive director of the Port Authority, “Should it have been caught? The answer is, probably.”

The temporary loading bays will add millions to the cost of One World Trade Center. The Wall Street Journal on Monday reported that the cost of the building has soared to $3.8 billion, $700 million more than the last publicly released estimate in 2008.

Foye said the soaring costs will be examined in a review of the agency that is being prepared for the governors of New York and New Jersey. He would not confirm the $3.8 billion figure.

Foye said the loading docks “a short-term issue.”

Other problems at the World Trade Center have included a dispute with the foundation that is building a 9/11 museum and financial troubles that have dogged the company that is laying steel.

Foye said the Port Authority still expects to finish One World Trade by the end of 2013.